Summary of Study ST002062
This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001283. The data can be accessed directly via it's Project DOI: 10.21228/M8VX1B This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.
| Study ID | ST002062 |
| Study Title | Endophytic bacteria are key players in the modulation of the secondary metabolome of Lithospermum officinale L. |
| Study Summary | Endophytic bacteria influence plant growth and development and therefore are an attractive resource for applications in agriculture. However, little is known about the impact of these microorganisms on secondary metabolite (SM) production by medicinal plants. Here we assessed, for the first time, the effects of root endophytic bacteria on the modulation of SMs in the medicinal plant Lithospermum officinale (Boraginaceae family), with a focus on the naphthoquinones alkannin/shikonin (A/S). The study was conducted using a newly developed in vitro system as well as in the greenhouse. Targeted and non-targeted metabolomics approaches were used and supported by expression analysis of the gene PGT, encoding a key enzyme in the A/S biosynthesis pathway. Three bacterial strains, Chitinophaga sp. R-73072, Xanthomonas sp. R-73098 and Pseudomonas sp. R-71838 induced a significant increase of diverse SMs, including A/S, in L. officinale in both systems, demonstrating the strength of our approach for screening A/S derivative-inducing bacteria. Our results highlight the impact of root-endophytic bacteria on secondary metabolism in plants and indicate that production of A/S derivatives in planta likely involves cross-modulation of different metabolic pathways that can be manipulated by bacterial endophytes. |
| Institute | Aristotle University of Thessaloniki |
| Last Name | Rodic |
| First Name | Nebojsa |
| Address | Stepe Stepanovica 5, Conoplja, Serbia |
| nebojsa.rodic@hotmail.com | |
| Phone | +381648766400 |
| Submit Date | 2021-08-11 |
| Num Groups | 7 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2022-01-31 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Combined analysis:
| Analysis ID | AN003361 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Thermo Vanquish |
| Column | Waters Acquity UPLC HSS C18 SB (100 x 2.1mm, 1.8um) |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Q Exactive Focus |
| Ion Mode | POSITIVE |
| Units | intensity units |
MS:
| MS ID: | MS003130 |
| Analysis ID: | AN003361 |
| Instrument Name: | Thermo Q Exactive Focus |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | The solvents used were ultrapure water (A) and methanol (B), both with 0.1% (v/v) formic acid. The gradient elution program was as follows: 0 min 95A/5B, 1 min 50A/50B, 8 min 0A/100B, 13 min 0A/100B, 13.01 min 95A/5B, 16 min 95A/5B. Data were acquired in positive ionisation mode, with the capillary temperature set to 320 oC using the instrument's MS/MS discovery feature. The normalised collision energy was set to 35 eV. The instrument control, acquisition and initial processing of the data were conducted by the Xcalibur software (version 4.1, Thermo Scientific, USA). Furthermore, data alignment and feature extraction were performed on the XCMS online platform (Huan et al., 2017). Identification of some detected compounds was performed using the software Compound Discoverer (version 3.2, Thermo Scientific, USA). |
| Ion Mode: | POSITIVE |
